Advances In Development Of Tools Research Articles

Plasmonic-Driven Regulation of Biomolecular Activity In Situ.

Selective and remote manipulation of activity for biomolecules, including protein, DNA, and lipids, is crucial to elucidate their molecular function and to develop biomedical applications. While advances in tool development, such as optogenetics, have significantly impacted these directions, the requirement for genetic modification significantly limits their therapeutic applications. Plasmonic nanoparticle heating has brought new opportunities to the field, as hot nanoparticles are unique point heat sources at the nanoscale. In this review, we summarize fundamental engineering problems such as plasmonic heating and the resulting biomolecular responses. We highlight the biological responses and applications of manipulating biomolecules and provide perspectives for future directions in the field.

Is Drosophila Dpp/BMP morphogen spreading required for wing patterning and growth?

Secreted signaling molecules act as morphogens to control patterning and growth in many developing tissues. Since locally produced morphogens spread to form a concentration gradient in the surrounding tissue, spreading is generally thought to be the key step in the non-autonomous actions. Here, we review recent advances in tool development to investigate morphogen function using the role of decapentaplegic (Dpp)/bone morphogenetic protein (BMP)-type ligandin the Drosophila wing disc as an example. By applying protein binder tools to distinguish between the roles of Dpp spreading and local Dpp signaling, we found that Dpp signaling in the source cells is important for wing patterning and growth but Dpp spreading from this source cells is not as strictly required as previously thought. Given recent studies showing unexpected requirements of long-range action of different morphogens, manipulating endogenous morphogen gradients by synthetic protein binder tools could shed more light on how morphogens act in developing tissues.

Single-molecule sequencing and optical mapping yields an improved genome of woodland strawberry (Fragaria vesca) with chromosome-scale contiguity.

BackgroundAlthough draft genomes are available for most agronomically important plant species, the majority are incomplete, highly fragmented, and often riddled with assembly and scaffolding errors. These assembly issues hinder advances in tool development for functional genomics and systems biology.FindingsHere we utilized a robust, cost-effective approach to produce high-quality reference genomes. We report a near-complete genome of diploid woodland strawberry (Fragaria vesca) using single-molecule real-time sequencing from Pacific Biosciences (PacBio). This assembly has a contig N50 length of ∼7.9 million base pairs (Mb), representing a ∼300-fold improvement of the previous version. The vast majority (>99.8%) of the assembly was anchored to 7 pseudomolecules using 2 sets of optical maps from Bionano Genomics. We obtained ∼24.96 Mb of sequence not present in the previous version of the F. vesca genome and produced an improved annotation that includes 1496 new genes. Comparative syntenic analyses uncovered numerous, large-scale scaffolding errors present in each chromosome in the previously published version of the F. vesca genome.ConclusionsOur results highlight the need to improve existing short-read based reference genomes. Furthermore, we demonstrate how genome quality impacts commonly used analyses for addressing both fundamental and applied biological questions.

Barriers in the brain: resolving dendritic spine morphology and compartmentalization.

Dendritic spines are micron-sized protrusions that harbor the majority of excitatory synapses in the central nervous system. The head of the spine is connected to the dendritic shaft by a 50–400 nm thin membrane tube, called the spine neck, which has been hypothesized to confine biochemical and electric signals within the spine compartment. Such compartmentalization could minimize interspinal crosstalk and thereby support spine-specific synapse plasticity. However, to what extent compartmentalization is governed by spine morphology, and in particular the diameter of the spine neck, has remained unresolved. Here, we review recent advances in tool development – both experimental and theoretical – that facilitate studying the role of the spine neck in compartmentalization. Special emphasis is given to recent advances in microscopy methods and quantitative modeling applications as we discuss compartmentalization of biochemical signals, membrane receptors and electrical signals in spines. Multidisciplinary approaches should help to answer how dendritic spine architecture affects the cellular and molecular processes required for synapse maintenance and modulation.

Analysis model of parameters affecting cutting performance in high-speed machining

Further progress in green cutting applications depends on the innovativeness of machine tools, advances in tool development, and, especially, more complex tool and cutting technologies. Therefore, this study analyzes the factors influencing high-speed cutting performance. Grey relational analysis and the Taguchi method are then incorporated in the experimental plan with high-speed milling of AISI H13 tool steel. Experimental results indicate that the contributions of tool grinding precision, geometric angle, and cutting conditions to the multiple quality characteristics of high-speed milling for AISI H13 tool steel are 11.75, 9.80, and 73.11 %, respectively. For rough machining, tool life and metal removal volume are the primary evaluation indicators and cutting parameters should be prioritized, especially cutting speed and feed per tooth. In finish machining, workpiece surface roughness is the primary evaluation indicator. Besides the selection of cutting parameters, the design and grinding of endmill are critical factors, especially the design and grinding of relief angles.

Basic Properties of Compressible MHD Turbulence: Implications for Molecular Clouds

Recent advances in understanding of the basic properties of compressible Magnetohydrodynamic (MHD) turbulence call for revisions of some of the generally accepted concepts. First, the MHD turbulence is not so messy as it is usually believed. In fact, the notion of strong nonlinear coupling of compressible and incompressible motions is not tenable. Alfven, slow and fast modes of MHD turbulence follow their own cascades and exhibit degrees of anisotropy consistent with theoretical expectations. Second, the fast decay of turbulence is not related to the compressibility of fluid. Rates of decay of compressible and incompressible motions are very similar. Third, the viscosity by neutrals does not suppress MHD turbulence in a partially ionized gas. Instead, MHD turbulence develops magnetic cascade at scales below the scale at which neutrals damp ordinary hydrodynamic motions. The implications of those changes of MHD turbulence paradigm for molecular clouds require further studies. Those studies can benefit from testing of theoretical predictions using new statistical techniques that utilize spectroscopic data. We briefly discuss advances in development of tools using which the statistics of turbulent velocity can be recovered from observations.